[R] CRAN (and crantastic) updates this week

[Crantastic]

CRAN (and crantastic) updates this week

New packages
------------

* alabama (2010.7-1)
  Ravi Varadhan
  http://crantastic.org/packages/alabama

  Augmented Lagrangian Adaptive Barrier Minimization Algorithm for
  optimizing smooth nonlinear objective functions with constraints.
  Linear or nonlinear equality and inequality constraints are allowed.

* BMS (0.2.5)
  Stefan Zeugner
  http://crantastic.org/packages/BMS

  Bayesian Model Averaging for univariate linear models under Zellner's
  g prior. Options include: fixed (BRIC, UIP, ...) and flexible g
  priors (Empirical Bayes, hyper-g), 5 kinds of model prior concepts,
  and model sampling via model enumeration or MCMC samplers
  (Metropolis-Hastings plain or reversible jump). Post-processing
  allows for inference according to different concepts (likelihood vs
  MCMC-based) and for plotting (posterior model size and coefficient
  densities, best models, model convergence, BMA comparison).

* compareGroups (0.1-3)
  Isaac Subirana
  http://crantastic.org/packages/compareGroups

  This package is meant to facilitate the construction of bivariate
  table (descriptives of several variables between groups) and
  generate reports in LaTeX or (CSV) plain text. Also, it includes a
  graphical interface to build these tables more easily.

* constrainedKriging (0.1.0)
  Christoph Hofer
  http://crantastic.org/packages/constrainedKriging

  The constrainedKriging package provides functions for efficient
  computations of nonlinear spatial predictions with local change of
  support. The package supplies functions for tow-dimensional spatial
  interpolation by constrained, covariance-matching constrained and
  universal (external drift) kriging for points or block of any shape
  for data with a nonstationary mean function and an isotropic weakly
  stationary variogram. The linear spatial interpolation methods,
  constrained and covariance-matching constrained kriging, provide
  approximately unbiased prediction for nonlinear target values under
  change of support. The constrainedKriging package extends the range
  of geostatistical tools available in R and provides a veritable
  alternative to conditional simulation for nonlinear spatial
  prediction problems with local change of support.

* dafs (1.0-34)
  James M. Curran
  http://crantastic.org/packages/dafs

  Data and miscellanea to support the book "Introduction to Data
  analysis with R for Forensic Scientists", Curran, J.M. 2010 CRC
  Press ISBN: 978-1-4200-8826-7

* dismo (0.5-1)
  Unknown
  http://crantastic.org/packages/dismo

  Functions for species distribution modeling, that is, predicting
  entire distributions form occurences at specific sites.

* gaussDiff (1.0)
  Henning Rust
  http://crantastic.org/packages/gaussDiff

  A collection difference measures for multivariate Gaussian probability
  density functions, such as the Euclidian mean, the Mahalanobis
  distance, the Kullback-Leibler divergence, the J-Coefficient, the
  Minkowski L2-distance, the Chi-square divergence and the Hellinger
  Coefficient.

* grt (0.1-1)
  Kazunaga Matsuki
  http://crantastic.org/packages/grt

  Functions to generate and analyze data for psychology experiments
  based on the General Recognition Theory.

* HDclassif (1.0)
  L.Berge
  http://crantastic.org/packages/HDclassif

  New disciminant analysis and data clustering methods for high
  dimensional data, based on the asumption that high-dimensional data
  live in different subspaces with low dimensionality proposing a new
  parametrization of the Gaussian mixture model which combines the
  ideas of dimension reduction and constraints on the model.

* pvclass (1.0)
  Niki Zumbrunnen
  http://crantastic.org/packages/pvclass

  Computes nonparametric p-values for the potential class memberships of
  new observations as well as cross-validated p-values for the
  training data. The p-values are based on permutation tests applied
  to an estimated Bayesian likelihood ratio, using a plug-in statistic
  for the Gaussian model, 'k nearest neighbors' or 'weighted nearest
  neighbors'. Additionally, it provides graphical displays and
  quantitative analyses of the p-values.

* rAverage (0.3-2)
  Stefano Noventa
  http://crantastic.org/packages/rAverage

  Parameter estimation for the Averaging model of Anderson's Information
  Integration Theory

* RGtk2Extras (0.0.1)
  Tom Taverner
  http://crantastic.org/packages/RGtk2Extras

  Useful add-ons for RGtk2

* rJython (0.0-2)
  Carlos J. Gil Bellosta
  http://crantastic.org/packages/rJython

  R interface to Python via Jython allowing R to call python code.

* rTOFsPRO (1.1)
  Dariya Malyarenko
  http://crantastic.org/packages/rTOFsPRO

  rTOFsPRO provides functions for signal processing of the linear TOF
  spectra to produce aligned peak intensity matrix (and peak
  positions)

* Runiversal (1.0)
  Mehmet Hakan Satman
  http://crantastic.org/packages/Runiversal

  This package contains some functions for converting R objects to Java
  style variables and XML. Generated Java code is interpretable by
  dynamic Java libraries such as Beanshell. Calling R externally and
  handling the Java or XML output is an other way to call R from other
  languages without native interfaces.

* splinesurv (0.6-14)
  Emmanuel Sharef
  http://crantastic.org/packages/splinesurv

  Utilities for nonparametric Bayesian analysis of clustered survival
  data. The baseline hazard function and frailty density are modeled
  using penalized B-splines. Options include adaptive knot selection
  and the inclusion of a parametric component.

* sprint (0.2.0)
  University of Edinburgh SPRINT Team
  http://crantastic.org/packages/sprint

  A simple framework for performing computation in parallel of R scripts
  and a library of parallelized R functions.

* VecStatGraphs3D (1.0)
  Juan Carlos Ruiz Cuetos
  http://crantastic.org/packages/VecStatGraphs3D

  This package performs a 3D statistical analysis, both numerical and
  graphic, of a set of vectors. Since a vector has three components (a
  module and two angles) vector analysis is performed in two stages:
  modules are analyzed by means of linear statistics and orientations
  are analyzed by spherical statistics. Tests and spherical statistic
  parameters have associated a full range of graphing: vector maps,
  density maps, distribution modules and angles. The tests, spherical
  statistic parameters and graphs allow us detecting another
  distribution properties (I.e. anisotropy) and outliers.

* WGCNA (0.92-3)
  Peter Langfelder
  http://crantastic.org/packages/WGCNA

  Functions necessary to perform Weighted Gene Co-Expression Network
  Analysis


Updated packages
----------------

ada (2.0-2), adegenet (1.2-5), AER (1.1-6), allan (1.01), amei
(1.0-4), aroma.affymetrix (1.7.0), aroma.core (1.7.0), aroma.light
(1.16.1), BaM (0.98), Bergm (1.3), BioPhysConnectoR (1.6-5), BioStatR
(1.0.1), BMS (0.2.5), candisc (0.5-18), car (2.0-0), car (2.0-1),
caret (4.45), caroline (0.2-0), CAVIAR (1.1-0), choplump (1.0-0.1),
DAAGxtras (0.7-9), DAAGxtras (0.7-8), ddst (1.02), DPpackage (1.1-1),
EnQuireR (0.10), exact2x2 (1.0-1.1), exactci (1.1-0.1), expm (0.98-2),
FactoClass (1.0.4), FieldSim (3.1.3), forecast (2.06), formula.tools
(1.0.1), fxregime (1.0-1), gee (4.13-15), genefu (1.0.8), geosphere
(1.2-7), geozoo (0.4.2), GEVcdn (1.0.1), GGally (0.2.1), granova
(1.4), grt (0.1-1), gWidgetsRGtk2 (0.0-68), gWidgetstcltk (0.0-39),
hda (0.1-10), heplots (0.9-3), hergm (1.2-7), HiddenMarkov (1.3-2),
HistData (0.6-9), inline (0.3.6), interval (1.0-0.0), IPSUR (1.0),
lmtest (0.9-27), MChtest (1.0-2), metafor (1.4-0), mixAK (1.1),
mixsmsn (0.2-6), mra (2.7), multtest (2.5.14), mvgraph (1.2), MVpower
(2.0), ncdf (1.6.2), ncdf (1.6.3), optmatch (0.7-0), ouch (2.7-1),
outliers (0.13-3), perm (1.0-0.0), perturb (2.04), phylobase (0.6.1),
plink (1.2-4), plspm (0.1-10), proftools (0.0-3), qpcR (1.2-9), qtl
(1.17-39), R.utils (1.4.4), raster (1.3-4), rattle (2.5.37), rAverage
(0.3-2), Rcmdr (1.6-0), RcmdrPlugin.SensoMineR (1.11-01), rconifers
(1.0.1), Rcpp (0.8.5), RcppArmadillo (0.2.4), RcppExamples (0.1.1),
relations (0.5-8), RHRV (2.5), rjags (2.1.0-6), rjson (0.2.0), RODBC
(1.3-2), rsm (1.40), rwm (1.51), scrime (1.2.1), season (0.2-5),
spatstat (1.20-1), spcosa (0.2-2), spdep (0.5-17), splinesurv
(0.6-14), strucchange (1.4-1), termstrc (1.3.2), textcat (0.0-4),
timeDate (2120.90), timeSeries (2120.89), tolerance (0.2.2), TSAgg
(0.1-9), TSP (1.0-1), ttime (1.2.2)

New reviews
-----------

* data.table, by branson.owen
  http://crantastic.org/reviews/82

* psych, by ch.lalanne
  http://crantastic.org/reviews/81

* DEoptim, by mhsatman
  http://crantastic.org/reviews/80



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